Contacts of the helix formed by residues 314 - 324 (chain A) in PDB entry 1CEZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312A TYR* 3.3 45.3 - - + +
313A MET* 1.3 90.2 - - - +
315A GLU* 1.3 68.0 + - + +
317A TYR* 3.5 6.7 + - + +
318A LYS* 3.0 31.3 + - + +
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313A MET 3.3 0.8 - - - -
314A PRO* 1.3 81.9 - - + +
316A VAL* 1.3 62.1 + - - +
318A LYS* 2.8 32.7 + - - +
319A ALA* 3.0 31.0 + - - +
731A ASP* 3.8 31.8 + - + +
792A ARG* 5.1 0.2 - - - +
793A LYS* 6.1 0.9 - - + -
796A VAL* 3.4 31.8 - - + +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A LEU* 5.5 0.9 - - + -
313A MET* 3.0 42.1 + - + +
315A GLU* 1.3 77.2 - - - +
317A TYR* 1.3 62.6 - - + +
319A ALA* 3.2 3.8 + - - +
320A ILE* 3.0 27.8 + - + +
420A MET* 3.4 35.7 - - + -
731A ASP* 4.1 17.9 - - - +
733A PHE* 4.0 30.7 - - + +
792A ARG* 4.3 10.3 - - - +
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Residues in contact with TYR 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TRP* 3.5 31.4 - - + +
279A THR* 3.7 7.4 - - - -
280A GLY* 3.3 49.0 - - - -
281A ILE* 3.7 2.3 + - - -
296A LEU* 3.7 22.4 - - + +
308A TYR* 4.9 6.2 + - - +
309A GLU 5.7 1.0 + - - -
312A TYR* 5.5 3.4 - - - -
313A MET* 3.3 50.8 + - + +
314A PRO* 4.0 7.0 - - + +
316A VAL* 1.3 80.1 - - + +
318A LYS* 1.3 57.3 + - - +
320A ILE* 3.9 5.1 - - - +
321A ASN* 2.9 39.5 + - - +
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Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314A PRO* 3.0 19.3 + - + +
315A GLU* 2.8 43.2 + - - +
317A TYR* 1.3 76.9 - - - +
319A ALA* 1.3 57.4 + - - +
321A ASN* 3.8 5.0 - - - +
322A ILE* 3.0 47.9 + - + +
796A VAL* 3.5 11.9 - - + -
800A GLU* 3.1 33.8 + - - +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLU 3.0 18.4 + - - +
316A VAL 3.5 3.8 - - - +
318A LYS* 1.3 74.0 - - - +
320A ILE* 1.3 66.8 + - - +
322A ILE* 3.0 13.2 + - - +
323A ALA* 3.1 14.3 + - - +
792A ARG* 3.6 46.4 - - + +
795A VAL* 3.9 11.1 - - + +
796A VAL* 4.0 7.4 - - + -
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Residues in contact with ILE 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TRP* 3.5 34.3 - - + +
296A LEU* 4.7 7.9 - - + -
316A VAL* 3.0 21.2 + - + +
317A TYR* 3.9 5.6 - - - +
319A ALA* 1.3 75.5 - - - +
321A ASN* 1.3 57.6 + - - +
323A ALA* 3.4 5.4 + - - +
324A GLN* 3.0 27.5 + - - +
418A TYR* 4.1 14.9 - - + +
419A ASN 4.3 5.6 - - - +
420A MET* 3.6 43.7 - - + -
426A VAL* 3.9 26.5 - - + -
792A ARG* 5.1 2.0 - - - -
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Residues in contact with ASN 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185A VAL* 6.0 1.0 - - - +
277A PRO* 3.7 13.3 - - + +
278A TRP* 2.8 62.5 + - - +
317A TYR* 2.9 24.0 + - - +
318A LYS* 3.9 5.3 - - - +
320A ILE* 1.3 74.0 - - - +
322A ILE* 1.3 66.0 + - + +
324A GLN* 3.6 10.2 + - - +
325A ASN* 3.2 22.9 + - - +
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Residues in contact with ILE 322 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318A LYS* 3.0 34.7 + - + +
319A ALA 3.0 4.0 + - - +
321A ASN* 1.3 75.4 - - + +
323A ALA* 1.3 68.4 + - - +
325A ASN* 3.2 17.6 + - - +
326A THR* 3.7 7.3 + - - -
795A VAL* 3.7 8.5 - - + -
796A VAL* 4.2 17.5 - - + +
799A HIS* 3.4 49.1 - - + +
800A GLU* 5.4 1.8 - - + +
805A GLU 4.6 3.8 - - - +
807A PHE* 3.7 29.4 - - + -
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Residues in contact with ALA 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ALA 3.1 14.6 + - - +
320A ILE* 3.9 6.1 - - - +
322A ILE* 1.3 78.8 - - - +
324A GLN* 1.3 63.9 + - - +
326A THR* 3.0 25.8 + - - +
418A TYR* 4.0 26.2 + - + -
426A VAL* 5.2 3.1 - - + -
795A VAL* 4.5 2.4 - - + +
807A PHE* 5.1 4.4 - - + +
809A LEU* 3.5 31.4 - - + -
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Residues in contact with GLN 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A PRO* 3.6 30.3 - - + +
276A LYS 3.2 20.5 - - - +
277A PRO* 4.0 1.0 - - - +
278A TRP* 2.9 34.7 - - - +
285A GLY* 3.8 3.0 - - - -
320A ILE 3.0 15.2 + - - +
321A ASN* 3.6 12.9 + - - +
323A ALA* 1.3 78.1 - - - +
325A ASN* 1.3 57.2 + - - +
326A THR 3.3 5.0 + - - +
415A TRP* 3.8 5.9 - - - +
416A PHE 3.5 25.9 + - - +
417A PRO* 3.4 14.5 - - + +
418A TYR* 2.8 29.1 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il